Your expectations and concerns are reasonable. Unfortunately, industry "standards" in your area will dictate what you can actually expect in a contract. Small startup companies will generally offer you the best price; long-term established contractors will offer you more security in terms of bonding, insurance, and warranty follow-through. A 10, 20 or 30 year warranty from a company which folds up its tents in 3 years is obviously worthless.
You should seek the lowest deposit possible, but anything below the prevailing rate in your area will be difficult to negotiate. The 50% deposit which you mentioned is fairly common. However, I personally believe that a reasonable deposit should consist of one or two hundred dollars "good faith deposit" followed by payments for actual expenses as they are actually accrued (materials and labor expenses at the time of expenditure). I also prefer a few days after completion before making the final payment. Otherwise, the purchaser has little clout in resolving disputes.
I've had 4 modestly expensive ($1000-$5000 each) exterior improvement contracts over the past few years and I've been fortunate enough to get all of them on COD terms. There was no down payment and payment in full was due immediately upon receipt of the invoice, which was generally
2 days after completion.
But this is a rare negotiation and I'd say that you are doing well if you can get by on a 25% deposit, 50% due on completion and the remaining
25% due 2 calendar days after completion. This gives you time to "walk the roof" (when it is cool!) and examine it for spongy areas, exposed nails, missing caulk, damaged shingles, bad flashing, etc. It also gives you time to test valleys with a garden hose if you desire before making that final payment. If you must pay in full upon completion, then let the contractor know that you want to walk the roof once or twice during construction and upon completion. Try to walk the roof along with the crew foreman so that you can discuss possible problems and also so that you will not be accused of causing any damage to the new roof.
Negotiating terms better than the prevailing rate for a deposit will be difficult but not impossible. A perfect credit rating is one of your strongest bargaining chip. So is ownership of multiple properties and/or any other indication that you may represent repeat business in the near future.
Warranty information should be very clearly spelled out in a contract. This should include more than just the manufacturer's warranty statement. Insurance, workman's comp and bonding information should be available upon request.
Rookie carpenters in my area make $10-$12 per hour and apprentice carpenters earn about $16-$20. Standard roofing crew seldom include anybody that I would rank much higher than apprentice carpenters. Of course, there is overhead and profit that must be tacked on top of those rate.
Generally, carpentry rates should be a factor only if there is structural damage due to leaks or if you are making major changes to your roof such as extending your roof lines to create an overhang. Resheathing costs should be flat-rated and clearly described in the contract as a contingency item at about $40-$55 total cost per sheet for removal, materials and installation. Anticipated carpentry work (installing ridge vents, etc.) should be part of your fixed cost estimate and included in the total price for the contract.
This is beyond the scope of your initial questions and request for advice, but you can always consider doing the roofing yourself, especially if you don't need a tearoff of the current shingles. Basic roofing is hard work and not rocket science. If you have one or two neighbors who also need new roofs, then you can form a team and attack one roof per weekend and probably complete one roof each Saturday. You can even save a bit on the trip charge for shingle delivery if the houses are close to one another. For about $50 per house, you can have the shingles delivered directly onto the roofs. Just worth considering.
Good luck, Gideon